Reassociation kinetics-based approach for partial genome sequencing of the cattle tick, Rhipicephalus (Boophilus) microplus

F.D. Guerrero; P. Moolhuijzen; D.G. Peterson; S. Bidwell; E. Caler; M. Bellgard; V.M. Nene; A. Djikeng

doi:10.1186/1471-2164-11-374

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Reassociation kinetics-based approach for partial genome sequencing of the cattle tick, Rhipicephalus (Boophilus) microplus

Journal article

Open access

Peer reviewed

Reassociation kinetics-based approach for partial genome sequencing of the cattle tick, Rhipicephalus (Boophilus) microplus

F.D. Guerrero, P. Moolhuijzen, D.G. Peterson, S. Bidwell, E. Caler, M. Bellgard, V.M. Nene and A. Djikeng

BMC Genomics, Vol.11(1)

2010

DOI: https://doi.org/10.1186/1471-2164-11-374

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Abstract

Background: The size and repetitive nature of the Rhipicephalus microplus genome makes obtaining a full genome sequence fiscally and technically problematic. To selectively obtain gene-enriched regions of this tick's genome, Cot filtration was performed, and Cot-filtered DNA was sequenced via 454 FLX pyrosequencing.Results: The sequenced Cot-filtered genomic DNA was assembled with an EST-based gene index of 14,586 unique entries where each EST served as a potential "seed" for scaffold formation. The new sequence assembly extended the lengths of 3,913 of the 14,586 gene index entries. Over half of the extensions corresponded to extensions of over 30 amino acids. To survey the repetitive elements in the tick genome, the complete sequences of five BAC clones were determined. Both Class I and II transposable elements were found. Comparison of the BAC and Cot filtration data indicates that Cot filtration was highly successful in filtering repetitive DNA out of the genomic DNA used in 454 sequencing.Conclusion: Cot filtration is a very useful strategy to incorporate into genome sequencing projects on organisms with large genome sizes and which contain high percentages of repetitive, difficult to assemble, genomic DNA. Combining the Cot selection approach with 454 sequencing and assembly with a pre-existing EST database as seeds resulted in extensions of 27% of the members of the EST database.

Details

Title: Reassociation kinetics-based approach for partial genome sequencing of the cattle tick, Rhipicephalus (Boophilus) microplus
Authors/Creators: F.D. Guerrero (Author/Creator) - Knipling-Bushland U.S. Livestock Insects Research Laboratory
P. Moolhuijzen (Author/Creator) - Murdoch University
D.G. Peterson (Author/Creator)
S. Bidwell (Author/Creator) - J. Craig Venter Institute
E. Caler (Author/Creator) - J. Craig Venter Institute
M. Bellgard (Author/Creator) - Murdoch University
V.M. Nene (Author/Creator) - International Livestock Research Institute
A. Djikeng (Author/Creator) - International Livestock Research Institute
Publication Details: BMC Genomics, Vol.11(1)
Publisher: BioMed Central
Identifiers: 991005545135707891
Copyright: © 2010 Guerrero et al
Murdoch Affiliation: Centre for Comparative Genomics
Language: English
Resource Type: Journal article
Note: This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Collaboration types: Domestic collaboration; International collaboration
Citation topics: 1 Clinical & Life Sciences; 1.258 Zoonotic Diseases; 1.258.227 Tick-borne Pathogens
Web Of Science research areas: Biotechnology & Applied Microbiology; Genetics & Heredity
ESI research areas: Molecular Biology & Genetics